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Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium.

Rouli L, MBengue M, Robert C, Ndiaye M, La Scola B, Raoult D - New Microbes New Infect (2014)

Bottom Line: We found that the three African strains contained the pX01 and pX02 plasmids, the nonsense mutation in the plcR gene and the four known prophages.We validated the hypothesis that B. anthracis has a closed pan-genome and found that the three African strains carry the two plasmids associated with bacterial virulence.Moreover, thanks to the study of the core content single nucleotide polymorphisms, we can see that our three African strains diverged very recently from the other B. anthracis strains.

View Article: PubMed Central - PubMed

Affiliation: Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France.

ABSTRACT
Bacillus anthracis is the causative agent of anthrax and is classified as a 'Category A' biological weapon. Six complete genomes of B. anthracis (A0248, Ames, Ames Ancestor, CDC684, H0491, and Sterne) are currently available. In this report, we add three African strain genomes: Sen2Col2, Sen3 and Gmb1. To study the pan-genome of B. anthracis, we used bioinformatics tools, such as Cluster of Orthologous Groups, and performed phylogenetic analysis. We found that the three African strains contained the pX01 and pX02 plasmids, the nonsense mutation in the plcR gene and the four known prophages. These strains are most similar to the CDC684 strain and belong to the A cluster. We estimated that the B. anthracis pan-genome has 2893 core genes (99% of the genome size) and 85 accessory genes. We validated the hypothesis that B. anthracis has a closed pan-genome and found that the three African strains carry the two plasmids associated with bacterial virulence. The pan-genome nature of B. anthracis confirms its lack of exchange (similar to Clostridium tetani) and supports its exclusively pathogenic role, despite its survival in the environment. Moreover, thanks to the study of the core content single nucleotide polymorphisms, we can see that our three African strains diverged very recently from the other B. anthracis strains.

No MeSH data available.


Related in: MedlinePlus

Summary of the Bacillus anthracis lifestyle.
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fig07: Summary of the Bacillus anthracis lifestyle.

Mentions: In comparing the three African strains to the other B. anthracis strains,we noticed that all of the African strains carried the two virulence plasmids (pX01 and pX02), theplcR nonsense mutation and four prophages. We also determined that these strainswere more closely related to CDC684 at the functional, sequence, plasmid and lineage levels. In thiswork, we validate the finding that, as previously shown 9, thepan-genome of B. anthracis is very narrow and thatB. anthracis is clonal. To have confidence in our study, we used manydifferent tools to compare and validate our results. All of the tools yielded the same results: theaddition of the three African strains did not change the nature of theB. anthracis pan-genome (2893 core genes and 85 accessory genes), which hada core/pan-genome ratio of 99%. This core/pan-genome ratio is very close to those from theother human clonal pathogens (Table1), such asRickettsia rickettsii. However, there is discordance between the presence of amobilome (some phages) and the fact that B. anthracis has a closedpan-genome. Nevertheless, B. anthracis is derived from theB. cereus group, a sympatric species that is not intracellular. Therefore,B. anthracis may have become entirely allopatric. Moreover, based on thecore genome, we found very few SNPs (896), a very small transition/transversion bias (0.32) and noCRISPRs. Hence, we can hypothesize that B. anthracis is an ancient clonethat evolved slowly. Indeed, the work of Mancini and Ippolito 33 describes the history of anthrax disease and suggested that the first case may date backto antiquity. However, calculating the age of this type of bacterium is difficult due to its lifecycle (a short vegetative phase of 20–40 generations and a long spore phase) 9. Bacillus anthracis does not replicate in thespore phase, and when it is in tissues, it may replicate as a pathogen to avoid living in sympatry.This behaviour is similar to Clostridium tetani34, a sporulating, anaerobic bacterium that resides in thesoil and is pathogenic for humans and animals. We recently obtained a new genome ofC. tetani and found that it is also very close to the reference genome 35. Therefore, the B. anthracis pathogenevolves very slowly compared with other species with similar generation times 18,19. We believe that the lack of genetransfer and defence mechanisms (CRISPRs) observed in intracellular bacteria 36 suggests that B. anthracis multiplies only as a pathogenand that its life in soil is exclusively dormant (Fig.7).


Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium.

Rouli L, MBengue M, Robert C, Ndiaye M, La Scola B, Raoult D - New Microbes New Infect (2014)

Summary of the Bacillus anthracis lifestyle.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4265047&req=5

fig07: Summary of the Bacillus anthracis lifestyle.
Mentions: In comparing the three African strains to the other B. anthracis strains,we noticed that all of the African strains carried the two virulence plasmids (pX01 and pX02), theplcR nonsense mutation and four prophages. We also determined that these strainswere more closely related to CDC684 at the functional, sequence, plasmid and lineage levels. In thiswork, we validate the finding that, as previously shown 9, thepan-genome of B. anthracis is very narrow and thatB. anthracis is clonal. To have confidence in our study, we used manydifferent tools to compare and validate our results. All of the tools yielded the same results: theaddition of the three African strains did not change the nature of theB. anthracis pan-genome (2893 core genes and 85 accessory genes), which hada core/pan-genome ratio of 99%. This core/pan-genome ratio is very close to those from theother human clonal pathogens (Table1), such asRickettsia rickettsii. However, there is discordance between the presence of amobilome (some phages) and the fact that B. anthracis has a closedpan-genome. Nevertheless, B. anthracis is derived from theB. cereus group, a sympatric species that is not intracellular. Therefore,B. anthracis may have become entirely allopatric. Moreover, based on thecore genome, we found very few SNPs (896), a very small transition/transversion bias (0.32) and noCRISPRs. Hence, we can hypothesize that B. anthracis is an ancient clonethat evolved slowly. Indeed, the work of Mancini and Ippolito 33 describes the history of anthrax disease and suggested that the first case may date backto antiquity. However, calculating the age of this type of bacterium is difficult due to its lifecycle (a short vegetative phase of 20–40 generations and a long spore phase) 9. Bacillus anthracis does not replicate in thespore phase, and when it is in tissues, it may replicate as a pathogen to avoid living in sympatry.This behaviour is similar to Clostridium tetani34, a sporulating, anaerobic bacterium that resides in thesoil and is pathogenic for humans and animals. We recently obtained a new genome ofC. tetani and found that it is also very close to the reference genome 35. Therefore, the B. anthracis pathogenevolves very slowly compared with other species with similar generation times 18,19. We believe that the lack of genetransfer and defence mechanisms (CRISPRs) observed in intracellular bacteria 36 suggests that B. anthracis multiplies only as a pathogenand that its life in soil is exclusively dormant (Fig.7).

Bottom Line: We found that the three African strains contained the pX01 and pX02 plasmids, the nonsense mutation in the plcR gene and the four known prophages.We validated the hypothesis that B. anthracis has a closed pan-genome and found that the three African strains carry the two plasmids associated with bacterial virulence.Moreover, thanks to the study of the core content single nucleotide polymorphisms, we can see that our three African strains diverged very recently from the other B. anthracis strains.

View Article: PubMed Central - PubMed

Affiliation: Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France.

ABSTRACT
Bacillus anthracis is the causative agent of anthrax and is classified as a 'Category A' biological weapon. Six complete genomes of B. anthracis (A0248, Ames, Ames Ancestor, CDC684, H0491, and Sterne) are currently available. In this report, we add three African strain genomes: Sen2Col2, Sen3 and Gmb1. To study the pan-genome of B. anthracis, we used bioinformatics tools, such as Cluster of Orthologous Groups, and performed phylogenetic analysis. We found that the three African strains contained the pX01 and pX02 plasmids, the nonsense mutation in the plcR gene and the four known prophages. These strains are most similar to the CDC684 strain and belong to the A cluster. We estimated that the B. anthracis pan-genome has 2893 core genes (99% of the genome size) and 85 accessory genes. We validated the hypothesis that B. anthracis has a closed pan-genome and found that the three African strains carry the two plasmids associated with bacterial virulence. The pan-genome nature of B. anthracis confirms its lack of exchange (similar to Clostridium tetani) and supports its exclusively pathogenic role, despite its survival in the environment. Moreover, thanks to the study of the core content single nucleotide polymorphisms, we can see that our three African strains diverged very recently from the other B. anthracis strains.

No MeSH data available.


Related in: MedlinePlus